That's not what this app is doing though. APFS clones are copy-on-write pointers to the same data, not hardlinks.
> clone: reflink-capable filesystems only. Try to clone both files with the FIDEDUPERANGE ioctl(3p) (or BTRFS_IOC_FILE_EXTENT_SAME on older kernels). This will free up duplicate extents while preserving the metadata of both. Needs at least kernel 4.2.